Unusually effective microRNA targeting within repeat-rich coding regions of mamalian mRNAs
Michael Schnall-Levin, Olivia Rissland, Wendy Johnston, Norbert Perrimon, David Bartel and Bonnie Berger
Genome Research (2011) http://genome.cshlp.org/content/early/2011/06/16/gr.121210.111?top=1
 
IsoBase: a database of functionally related proteins across PPI Networks
Daniel Park, Rohit Singh, Michael Baym, Chung-Shou Liao and Bonnie Berger
Nucleic Acids Research (2011) 39, (suppl 1): D295-D300  http://nar.oxfordjournals.org/content/39/suppl_1/D295.abstract

Identification of functional elements and regulatory circuits by drosophila modENCODE
The ModEncode Consortium
Science (2010) 330:6012, 1787-1797 DOI: 10.1126/science.1198374

Conserved microRNA targeting in drosophila is as widespread in coding regions as in 3' UTRs
Michael Schnall-Levin, Yong Zhao, Norbert Perrimon and Bonnie Berger
Proceedings of the National Academy of Sciences (2010) 107:36, 15751-15756

Local optimization for the global alignment of protein interaction networks
Leonid Chindelevitch, Chung-Shou Liao and Bonnie Berger
Pacific Symposium on Biocomputing (2010) p.123-132 10.1142/9789814295291_0015


Simultaneous alignment and folding of protein sequences
Jerome Waldispuhl, Charles W. O'Donnell, Sebastian Will, Srinivas Devadas, Rolf Backofen and Bonnie Berger

Lecture Notes in Computer Science, Research in Computational Molecular Biology, Vol. 5541/2009, p. 339-355, 2009. http://dx.doi.org/10.1007/978-3-642-02008-7_25

IsoRankN: spectral methods for global alignment of multiple protein networks 
Chung-Shou Liao, Kanghao Lu, Michael Baym, Rohit Singh, and Bonnie Berger
Bioinformatics 2009 25: i253 - i258.

IsoRank: Global alignment of multiple protein interaction networks with applications to functional orthology detection
Rohit Singh, Jinbo Xu and Bonnie Berger
Proceedings of the National Academy of Sciences (2008) 105:35, 12763-12768.   
http://www.pnas.org/content/105/35/12763.full

Pairwise global alignment of protein interaction networks by matching neighborhood topology
  Rohit Singh, Jinbo Xu and Bonnie Berger
  Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (2007): Lecture Notes in Computer Science  4453, 16-31.
abstract bibTeX citation   publisher's site

  Methods in comparative genomics: genome correspondence, gene identification, and motif discovery
Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger , and Eric S. Lander
Journal of Computational Biology (2004) 11 no.2-3, 319-355.
 

 bibTeX citation

  MSARi: Multiple sequence alignments for statistical detection of RNA secondary structure
 Alex Coventry, Daniel J. Kleitman, and Bonnie Berger
  Proceedings of the National Academy of Sciences (2004) 101 no. 33, 12102-12107.

abstract

 bibTeX citation

publisher's site

  Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species
 Manolis Kellis (Kamvysselis), Nick Patterson , Bruce Birren , Bonnie Berger, and Eric Lander
 In Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology RECOMB (2003) 157-166.
abstract  bibTeX citation publisher's site

  ARACHNE: A whole-genome shotgun assembler
 Serafim Batzoglou , David B. Jaffe , Ken Stanley , Jonathan Butler , Sante Gnerre , Evan Mauceli , Bonnie Berger , Jill P. Mesirov , and Eric S. Lander
 Genome Research (2002 ) 12 no. 1, 177 -189.
abstract  bibTeX citation publisher's site

  Human and mouse gene structure: comparative analysis and application to exon prediction
 Serafim Batzoglou, Lior Pachter, Jill Mesirov, Bonnie Berger, and Eric S. Lander
 Genome Research (2000) 10, 950-958.
abstract  bibTeX citation publisher's site

  Sequencing a genome by walking with clone-end sequences: a mathematical analysis
 Serafim Batzoglou, Bonnie Berger, Jill Mesirov, and Eric S. Lander
 Genome Research (1999) 9 no. 12, 1163-1174.
abstract  bibTeX citation publisher's site

  A dictionary based approach for gene annotation
 Lior Pachter, Serafim Batzoglou, Valentin Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, and Bonnie Berger
 Journal of Computational Biology (1999) 6 no. 3, 419-430.
 

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  Recent developments in computational gene recognition
 Serafim Batzoglou, Bonnie Berger, Daniel J. Kleitman, Eric S. Lander, and Lior Pachter
 Documenta Mathematica: Journal der Deutschen Mathematiker-Vereinigung (1998) Extra Volume ICM I, 649-658.
abstract  bibTeX citation publisher's site

Revealing the spatial distribution of a disease while preserving privacy
Shannon Wieland, Christopher Cassa, Kenneth Mandl and Bonnie Berger
Proceedings of the National Academy of Sciences (2008) 105:46, 17608-17613.

Automated real time constant-specificity surveillance for disease outbreaks
Shannon C Wieland, John S Brownstein, Bonnie Berger and Kenneth D Mandl
BMC Medical Informatics and Decision Making (2007) 7, 15.
abstract    

Density-equalizing euclidean minimum spanning trees for the dectection of all disease cluster shapes
Shannon C Wieland, John S Brownstein, Bonnie Berger and Kenneth D Mandl
Proceedings of the National Academy of Sciences (2007) 104, 9404-9409.
abstract    

Constant specificity surveillance for real-time outbreak detection
Shannon C. Wieland, Bonnie Berger and Ken D. Mandl
MMWR Morb Mortal Wkly Rep (2005) 54 Suppl, 206.
abstract  bibTeX citation